RetrogeneDB ID: retro_opri_1124

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_75119:1468..1885(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000016146
• Aliases: None
• Description: None

Sequence

>retro_opri_1124
GCTGTCCCTGTACGCGCTGCACCGCGCGCCCGGGACCGGGACTACCGCGCGCTCTGCGACGTGGGCTCCGCCATCAGCTG
TTCTCGCGTCTTCTCGTCCAGATGGGGCCGGGGCTTCGGGCTGGTGGAGCAAGTCTTGGGCCAGGATAGCATCCTCAATC
AATCCAACAGTATATTCGGTTGCATTTTCTACACGCTGCAGCTGGCCTTAGGTTGCCTGCGGGCTCGCTGGGCCTCCATC
CTGCTGGTACTGAGCTCGCTGGTGTCGATTGCCGGTTCCGTCTACCTGGCCTGGATCCTGTTTTTCGTGCTCTATGATTT
CTGCATCGTTTGCATCACTACGTATGCCATCAACGTGGGCCTGATGTTGCTCAGCTTCCGGGAGGTCCCAGAACCCCAGG
TCAAGGCCAAGGGCCAC

Alignment

ORF - retro_opri_1124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.12 %
• Parental protein coverage: 85.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALHVKAA-RARDRDYRALCDVGSAISCSRVFSSRWGRGFGLVEQVLGQDSILNQSNSIFGCIFYTLQLAL
          A..V.AA.RARDRDYRALCDVGSAISCSRVFSSRWGRGFGLVEQVLGQDSILNQSNSIFGCIFYTLQLAL
Retrocopy AVPVRAAPRARDRDYRALCDVGSAISCSRVFSSRWGRGFGLVEQVLGQDSILNQSNSIFGCIFYTLQLAL

Parental  GCLRARWASILLVLSSLVSIAGSVYLAWILFFVLYDFCIVCITTYAINVGLMLLSFREVPEPQVKAKGH
          GCLRARWASILLVLSSLVSIAGSVYLAWILFFVLYDFCIVCITTYAINVGLMLLSFREVPEPQVKAKGH
Retrocopy GCLRARWASILLVLSSLVSIAGSVYLAWILFFVLYDFCIVCITTYAINVGLMLLSFREVPEPQVKAKGH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_1124 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003097	1 retrocopy	retro_cjac_4049,
Homo sapiens	ENSG00000167397	1 retrocopy	retro_hsap_4664,
Oryctolagus cuniculus	ENSOCUG00000002289	1 retrocopy	retro_ocun_1423,
Ochotona princeps	ENSOPRG00000016146	3 retrocopies	retro_opri_1124 , retro_opri_1164, retro_opri_70,
Pongo abelii	ENSPPYG00000007306	1 retrocopy	retro_pabe_3624,
Pan troglodytes	ENSPTRG00000008031	1 retrocopy	retro_ptro_3099,